similar to: Defining the "random" term in function "negbin" of AOD package

I'm attempting to run 250 permutations of a negative binomial GLM model for data on fish counts. Many of the models are fit appropriately, but some issue warnings such as "convergence not reached" or "step size truncated due to divergence." I've attempted using glm.nb from the MASS package and the negbin function from the AOD package, but both still cause some models to

Hi, When modeling with negbin from the aod package, parameters for a given count y | lambda~Poisson(lambda) with lambda following a Gamma distribution Gamma(r, theta) are estimated. The intercept is called phi. Some other parameters may be also be estimated from factors in the data: the estimates returned for all these would be in accordance with the Value listing in the negbin entry in the aod

I have fitted the faults.data to glm.nb and to the function negbin from the package aod. The output of both is the following: summary(glm.nb(n~ll, data=faults)) Call: glm.nb(formula = n ~ ll, data = faults, init.theta = 8.667407437, link = log) Deviance Residuals: Min 1Q Median 3Q Max -2.0470 -0.7815 -0.1723 0.4275 2.0896 Coefficients:

Edward, you also can use the package aod on CRAN, see the help page of the function negbin. Best Matthieu An example: > library(aod) > data(dja) > negbin(y ~ group + offset(log(trisk)), ~group, dja, fixpar = list(4, 0)) Negative-binomial model ----------------------- negbin(formula = y ~ group + offset(log(trisk)), random = ~group, data = dja, fixpar = list(4, 0))

Dear Lister, I am facing a strange problem fitting a GLM of the negative binomial family. Actually, I tried to estimate theta (the scale parameter) through glm.nb from MASS and could get convergence only relaxing the convergence tolerance to 1e-3. With warning messages: glm1<-glm.nb(nbcas~.,data=zonesdb4,control=glm.control(epsilon = 1e-3)) There were 25 warnings (use warnings() to see

hi all- I am doing some research, have never used R before until today and need to understand the following program for a project. if some one could PLEASE help me understand this program ASAP i would GREATLY appreciate it (any syntax/ statistic comments would be great) PLEASE PLEASE HELP!! THANKYOU!!! -on a side note, it seems to me that R doesnt include the pv, and it was calculated

Information on package 'aod' Description: Package: aod Version: 1.1-2 Date: 2005-06-08 Title: Analysis of Overdispersed Data Author: Matthieu Lesnoff <matthieu.lesnoff at cirad.fr> and Renaud Lancelot <renaud.lancelot at cirad.fr> Maintainer: Renaud Lancelot <renaud.lancelot at cirad.fr> Depends: R (>=

Information on package 'aod' Description: Package: aod Version: 1.1-2 Date: 2005-06-08 Title: Analysis of Overdispersed Data Author: Matthieu Lesnoff <matthieu.lesnoff at cirad.fr> and Renaud Lancelot <renaud.lancelot at cirad.fr> Maintainer: Renaud Lancelot <renaud.lancelot at cirad.fr> Depends: R (>=

Hi all, I haven't been able to find how to assess a variable who's name is constructed with paste. The problem is following: In a data frame, there are 12 columns whose title vary only by a digit, all other part being equal. I would like to compute a operation on a subset these variables and parse them in turn. the data frame "basin.param" contains columns called ratio1,

Dear all, I wonder if anyone can help me with specifying a right model for my analysis. I am a beginner to lme methods. I was unfortunately not able to find a solution to my problem on my own. Data structure: I have sampled monthly 6 basins during two hydrological cycles, and I have taken several (2 to 4) samples (“replicate”) for each basin and month. I’m trying to relate Shannon diversity

Hi, I wonder if predict.gam is supposed to work with family=negbin() definition? It seems to me that the values returned by type="response" are far off the observed values. Here is an example output from the negbin examples: > set.seed(3) > n<-400 > dat<-gamSim(1,n=n) > g<-exp(dat$f/5) > dat$y<-rnbinom(g,size=3,mu=g) >

Dear R people, I am not sure if this is the correct place to tell about problems in evolving programmes, but it seems that the `summary.negbin' function of the excellent `MASS' library is now broken, and gives the following error message: > summary(hm) Error in summary.negbin(hm) : subscript out of bounds `summary.negbin' calls `summary.glm' which seems to work and give the

One of many scripts to produce 4 lattice plots on one page keeps throwing an error. I've tried manipulating the file to eliminate the error, but have not been able to do so. The error is: > source('bicarb.R') Error in source("bicarb.R") : bicarb.R:15:1: unexpected symbol 14: 15: hco33 ^ The 'h' is in column 0 so the caret would be column -1, but it's

Can anyone help me? I''m having problems with the following code where I want to test the null hypothesis that regression slopes are the same among regressions. Here''s the code I''ve written with comments that include the final error I get. ... initial.dir <- getwd() library(systemfit) library(multcomp) basdata <- read.table("data_into7_test.txt",

Dear R-collegues, I'm getting an error message (Error in round) when summarising a glm.nb model, and when using anova.negbin (in R 1.3.1 for windows): > m.nb <- glm.nb(tax ~ areal) > m.bn Call: glm.nb(formula = tax ~ areal, init.theta = 5.08829537115498, link = log) Coefficients: (Intercept) areal 3.03146 0.03182 Degrees of Freedom: 283 Total (i.e. Null); 282

Dear Clara, Thanks for the reply. I am forwarding your message to the list, ok. When I wrote was a way of get further information to help the helpers. happy holidays, milton ---------- Forwarded message ---------- From: Clara Brück <clara_brueck@web.de> Date: 2009/12/30 Subject: Re: [R] Negbin Error Warnings To: milton ruser <milton.ruser@gmail.com> Dear Milton, Thanks for

Hi, I ran a negative binomial regression (NBR) using the Zelig-package and the negbin model. When I then try to use the simumlation approach using the setx () and sim() functions to calculate expected values and first difference for different levels of one of my independent variables, I get 50 errors warnings, telling me that the calculation rpois produced NAs. However, the data I use

I'm not sure I'm barking up the right tree here, but would I need to make use of groups to plot two separate datasets within ONE panel in xyplot? The desired end result is a single xy plot of two separate (but similar in values and ranges). Full code follows, xyplot code at bottom #########Determine Frequencies ##########coastal_slope #needs the maptools package to read ESRI grid

I am new to the R language. I am trying to plot multiple figures on one page through a loop, but the code just produce one graph on one page. Can someone show some light on what's wrong? Here is my code: library("quantreg") tcdata<-read.table("mydata.txt",header=TRUE) postscript("myfigure.ps") basins<-

This is my first time running GAMs in R. My csv file has these column headings: "X" "Y" "Sound" "Atlantic" "Blacktip" "Bonnet" "Bull" "Finetooth" "Lemon" "Scalloped" "Sandbar" "Spinner" "Abundance" "Diversity"